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Crystal structure of DIMT1 in complex with 5'-methylthioadenosine and adenosine from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8X3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 0.2 M Zinc Acetate Dihydrate, 0.1 M Sodium Cacodylate Trihydrate pH 6.5, 18% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.65 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.38 α = 90 b = 77.26 β = 119.95 c = 94.229 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2022-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.35 81.64 99.9 0.057 0.067 0.034 0.998 18.7 3.8 31324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 99.1 0.2 0.235 0.122 0.95 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.35 62.16 29766 1558 99.91 0.16682 0.16478 0.1727 0.20542 0.2131 RANDOM 32.536
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.61 0.44 -0.85 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.092 r_dihedral_angle_2_deg 9.205 r_long_range_B_refined 7.824 r_long_range_B_other 7.746 r_dihedral_angle_1_deg 7.121 r_scangle_other 5.657 r_scbond_it 3.549 r_scbond_other 3.549 r_mcangle_it 3.258 r_mcangle_other 3.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.092 r_dihedral_angle_2_deg 9.205 r_long_range_B_refined 7.824 r_long_range_B_other 7.746 r_dihedral_angle_1_deg 7.121 r_scangle_other 5.657 r_scbond_it 3.549 r_scbond_other 3.549 r_mcangle_it 3.258 r_mcangle_other 3.258 r_mcbond_it 2.1 r_mcbond_other 2.089 r_angle_refined_deg 1.516 r_angle_other_deg 0.494 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction